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Updated: Aug 23, 2026

Modeling Ligands into Maps Derived from Electron Cryomicroscopy
Published on: July 19, 2024
Use of electron density critical points as chemical function-based reduced representations of pharmacological ligands
John Binamé1, Nathalie Meurice, Laurence Leherte
1Laboratoire de Physico-Chimie Informatique, Facultés Universitaires Notre-Dame de la Paix, 61 Rue de Bruxelles, B-5000 Namur, Belgium.
Abstract:
In this paper, we propose a reduced representation of molecules of pharmacological interest based on their chemical functions. The proposed representations of the molecules are obtained by a topological analysis of their electron density maps at medium resolution, leading to graphs of critical points. The distribution of the different types of critical points are compared at various levels of resolution for a training set of 22 molecules in order to define the optimal resolution level leading to the best representation of the various chemical functions. The reduced representations can in the future be used for molecular similarity research and pharmacophore proposals.
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